Preparation and characterization of protein-nanotube ...
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Santa Clara University Scholar Commons Bioengineering School of Engineering 2009 Preparation and characterization of protein- nanotube conjugates Jonathan S. Dordick Dhiral A. Shah Ravindra C. Pangule Shyam Sundhar Bale Prashanth Asuri Santa Clara University, [email protected] See next page for additional authors Follow this and additional works at: hps://scholarcommons.scu.edu/bio_eng Part of the Biomedical Engineering and Bioengineering Commons Reproduced by permission from Kaushal Rege and Igor Medintz, Methods in Bioengineering: Nanoscale Bioengineering and Nanomedicine, Norwood, MA: Artech House, Inc., 2009. © 2009 by Artech House, Inc. is Book Chapter is brought to you for free and open access by the School of Engineering at Scholar Commons. It has been accepted for inclusion in Bioengineering by an authorized administrator of Scholar Commons. For more information, please contact [email protected]. Recommended Citation Shah, D.A, Pangule, R.C., Bale, S.S., Asuri, P., Joshi, A., Banerjee, A., … Kane, R.S. (2009). Preparation and characterization of protein-nanotube conjugates. In Methods in Bioengineering: Nanoscale Bioengineering and Nanomedicine (pp. 1–23). Artech House.
Transcript of Preparation and characterization of protein-nanotube ...
Santa Clara UniversityScholar Commons
Bioengineering School of Engineering
2009
Preparation and characterization of protein-nanotube conjugatesJonathan S. Dordick
Dhiral A. Shah
Ravindra C. Pangule
Shyam Sundhar Bale
Prashanth AsuriSanta Clara University, [email protected]
See next page for additional authors
Follow this and additional works at: https://scholarcommons.scu.edu/bio_eng
Part of the Biomedical Engineering and Bioengineering Commons
Reproduced by permission from Kaushal Rege and Igor Medintz, Methods in Bioengineering: Nanoscale Bioengineering and Nanomedicine, Norwood,MA: Artech House, Inc., 2009. © 2009 by Artech House, Inc.
This Book Chapter is brought to you for free and open access by the School of Engineering at Scholar Commons. It has been accepted for inclusion inBioengineering by an authorized administrator of Scholar Commons. For more information, please contact [email protected].
Recommended CitationShah, D.A, Pangule, R.C., Bale, S.S., Asuri, P., Joshi, A., Banerjee, A., … Kane, R.S. (2009). Preparation and characterization ofprotein-nanotube conjugates. In Methods in Bioengineering: Nanoscale Bioengineering and Nanomedicine (pp. 1–23). ArtechHouse.
AuthorsJonathan S. Dordick, Dhiral A. Shah, Ravindra C. Pangule, Shyam Sundhar Bale, Prashanth Asuri, Amit Joshi,Akhilesh Banerjee, David Vance, and Ravi S. Kane
This book chapter is available at Scholar Commons: https://scholarcommons.scu.edu/bio_eng/29
Methods in BioengineeringNanoscale Bioengineering and Nanomedicine
Kaushal RegeDepartment of Chemical EngineeringArizona State University
Igor L. MedintzCenter for Biomolecular Science and EngineeringU.S. Naval Research Laboratory
Editors
a r techhouse . com
Library of Congress Cataloging-in-Publication DataA catalog record for this book is available from the U. S. Library of Congress.
British Library Cataloguing in Publication DataA catalogue record for this book is available from the British Library.
ISBN-13: 978-1-59693-410-8
Text design by Darrell JuddCover design by Igor Valdman
© 2009 Artech House. All rights reserved.
Printed and bound in the United States of America. No part of this book may be reproduced orutilized in any form or by any means, electronic or mechanical, including photocopying, record-ing, or by any information storage and retrieval system, without permission in writing from thepublisher.
All terms mentioned in this book that are known to be trademarks or service marks have beenappropriately capitalized. Artech House cannot attest to the accuracy of this information. Use ofa term in this book should not be regarded as affecting the validity of any trademark or servicemark.
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Contents
Preface xv
CHAPTER 1Preparation and Characterization of Carbon Nanotube-Protein Conjugates 1
1.1 Introduction 2
1.2 Materials 3
1.3 Methods 3
1.3.1 Physical Adsorption of Proteins on Carbon Nanotubes 3
1.3.2 Protein Assisted Solubilization of Carbon Nanotubes 4
1.3.3 Covalent Attachment of Proteins onto Carbon Nanotubes 5
1.4 Data Acquisition, Anticipated Results, and Interpretation of Data 7
1.4.1 Characterization of Proteins Physically Adsorbed onto1.4.1 Carbon Nanotubes 7
1.4.2 Characterization of Protein-Solubilized Carbon Nanotubes 11
1.4.3 Characterization of Covalently Attached Carbon1.4.1 Nanotube-Protein Conjugates 13
1.5 Discussion and Commentary 18
1.6 Applications Notes 19
1.7 Summary Points 21
Acknowledgments 21
References 21
CHAPTER 2Peptide-Nanoparticle Assemblies 25
2.1 Introduction 26
2.2 Materials 27
2.3 Methods 28
2.3.1 Coil-Coil Peptide Mediated NP Assembly 28
2.3.2 Synthesis of Hybrid Structures Using Multifunctional Peptides 31
2.4 Assembly Mediated by Metal Ion-Peptide Recognition 32
2.5 Peptides as Antibody Epitopes for Nanoparticle Assembly 33
2.6 DATA Acquisition, Anticipated Results, and Interpretation 34
2.7 Discussion and Commentary 35
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2.8 Application Notes 36
2.9 Summary Points 36
Acknowledgments 36
References 37
CHAPTER 3Nanoparticle-Enzyme Hybrids as Bioactive Materials 39
3.1 Introduction 40
3.2 Materials 40
3.3 Methods 41
3.3.1 Enzyme-Attached Polystyrene Nanoparticles 41
3.3.2 Polyacrylamide Hydrogel Nanoparticles for3.3.2 Entrapment of Enzymes 41
3.3.3 Magnetic Nanoparticles with Porous Silica Coating for3.3.3 Enzyme Attachment 42
3.3.4 Enzyme Loading and Activity Assay 42
3.4 Results 44
3.4.1 Polystyrene-Enzyme Hybrid Nanoparticles 44
3.4.2 Polyacrylamide Hydrogel Nanoparticles with3.4.2 Entrapped Enzymes 45
3.4.3 Magnetic Nanoparticles for Enzyme Attachment 46
3.5 Discussion and Commentary 47
3.6 Troubleshooting 49
3.7 Application Notes 49
3.8 Summary Points 49
Acknowledgments 50
References 50
CHAPTER 4Self-Assembled QD-Protein Bioconjugates and Their Use in FluorescenceResonance Energy Transfer 53
4.1 Introduction 54
4.2 Materials 56
4.2.1 Reagents 56
4.2.2 Equipment 56
4.3 Methods 56
4.3.1 Quantum Dot Synthesis 56
4.3.2 Surface Ligand Exchange 58
4.3.3 Biomolecule Conjugation 61
4.3.4 Fluorescence Measurements 65
4.4 Data Analysis and Interpretation 66
4.4.1 Calculating Donor-Acceptor Distances 68
4.4.2 Calculating Reaction Rates of Surface-Bound Substrates 70
Contents
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4.5 Summary Points 72
4.6 Conclusions 72
References 72
Annotated References 74
CHAPTER 5Tracking Single Biomolecules in Live Cells Using Quantum Dot Nanoparticles 75
5.1 Introduction 76
5.2 Materials 78
5.2.1 Reagents 78
5.2.2 Imaging Equipment 79
5.3 Methods 79
5.3.1 Forming QD Bioconjugates 79
5.3.2 Treating Cells with QD Bioconjugates 79
5.4 Data Acquisition, Anticipated Results, and Interpretation 79
5.4.1 Imaging QD-Bound Complexes in Cells 79
5.4.2 Analysis of the Real-Time QD Dynamics 80
5.5 Discussion and Commentary 81
References 82
CHAPTER 6Nanoparticles as Biodynamic Substrates for Engineering Cell Fates 85
6.1 Introduction 86
6.2 Experimental Design 88
6.3 Materials 88
6.3.1 Cell Culture, Fixing, Staining, and Analysis Reagents 88
6.3.2 Nanoparticle Fabrication and Functionalization 89
6.3.3 Microscale Plasma Initiated Patterning 89
6.4 Methods 89
6.4.1 Albumin Nanoparticle Fabrication 89
6.4.2 Albumin Nanoparticle Functionalization 91
6.4.3 Albumin Nanoparticle Pattern Creation—Microscale6.4.3 Plasma Initiated Patterning (μPIP) 93
6.4.4 Cell Culture 94
6.4.5 Keratinocyte Morphology and Migration 94
6.4.6 Fibroblast Extracellular Matrix Assembly 94
6.4.7 Cell Attachment Assay 95
6.5 Results 95
6.5.1 Enhanced Cell Migration 95
6.5.2 Enhanced Extracellular Matrix Assembly 97
6.6 Discussion of Pitfalls 100
6.6.1 Spatial Guidance of Cell Attachment—Microscale Plasma6.6.1 Initiated Patterning 100
Contents
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6.6.2 Three-Dimensional Presentation of Albumin Nanoparticles 101
6.7 Summary Points 102
Acknowledgments 103
References 103
CHAPTER 7Magnetic Cell Separation to Enrich for Rare Cells 107
7.1 Introduction 108
7.1.1 Principle 110
7.1.2 Examples of Cell Magnetic Separation Applications 115
7.2 Materials and Methods 116
7.2.1 Enrichment Process 116
7.2.2 Red Cell Lysis Step 117
7.2.3 Immunomagnetic Labeling 117
7.2.4 Magnetic Cell Separation Step 117
7.3 Data Acquisition, Results, and Interpretation 117
7.4 Discussion and Commentary 120
7.5 Summary Points to Obtain High-Performance,7.5 Magnetic Cell Separations 120
Acknowledgments 120
References 121
CHAPTER 8Magnetic Nanoparticles for Drug Delivery 123
8.1 Introduction 124
8.2 Experimental Design 124
8.3 Materials 126
8.3.1 Reagents 126
8.3.2 Facilities and Equipment 127
8.4 Methods 128
8.4.1 Synthesis of Magnetic Nanoparticles 128
8.4.2 Physical Characterization of Magnetic Nanoparticles 129
8.4.3 Conversion of DOX•HCl 129
8.4.4 Drug Loading and Release Kinetics 129
8.4.5 Kinetics of DOX Release from Magnetic Nanoparticles 130
8.4.6 Antiproliferative Activity of Doxorubicin Loaded Magnetic8.4.6 Nanoparticles on MCF-7 Cells 131
8.4.7 Antiproliferative Activity of Doxorubicin Loaded Magnetic8.4.6 Nanoparticles on MCF-7 Cells in the Presence of a8.4.6 Magnetic Field 131
8.5 Data Acquisition, Anticipated Results, and Interpretation 132
8.6 Discussion and Commentary 133
8.7 Application Notes 134
Contents
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8.8 Summary Points 134
Acknowledgments 135
References 135
CHAPTER 9Imaging and Therapy of Atherosclerotic Lesions with Theranostic Nanoparticles 137
9.1 Introduction 138
9.2 Experimental Design 139
9.3 Materials 140
9.3.1 Reagents 140
9.3.2 Facilities/Equipment 140
9.3.3 Animal Model 141
9.3.4 Alternate Reagents and Equipment 141
9.4 Methods 141
9.4.1 Synthesis of Theranostic Nanoparticles 141
9.4.2 Intravital Fluorescence Microscopy 143
9.4.3 Light-Based Therapy 144
9.5 Data Acquisition, Anticipated Results, and Interpretation 145
9.5.1 Characterization of Theranostic Nanoparticles 145
9.5.2 Animal Experimentation 146
9.5.3 Intravital Fluorescence Microscopy 146
9.5.4 Statistical Analyses 147
9.5.5 Anticipated Results 148
9.6 Discussion and Commentary 148
9.7 Summary Points 149
Acknowledgments 150
References 150
CHAPTER 10Biomedical Applications of Metal Nanoshells 153
10.1 Introduction 154
10.1.1 Biomedical Applications of Metal Nanoshells 154
10.1.2 Nanoshells for Combined Optical Contrast and10.1.2 Therapeutic Application 155
10.2 Experimental Design 156
10.3 Materials 156
10.3.1 Nanoparticle Production 156
10.3.2 Protein Conjugation to Nanoshells Surface 156
10.3.3 Cell Culture 157
10.3.4 In Vitro Assays 157
10.4 Methods 157
10.4.1 Fabrication of Gold/Silica Core Nanoshells 157
10.4.2 Nanoshells for Combined Imaging and Therapy In Vivo 158
Contents
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10.4.3 Passivation of Nanoshells with PEG 159
10.4.4 Conjugation of Biomolecules to Nanoshells 160
10.4.5 Quantification of Antibodies on Nanoshells 160
10.5 Results 161
10.5.1 Gold/Silica Nanoshells Allow Both Imaging Contrast Increase10.5.1 and Therapeutic Benefit 161
10.5.2 Evaluation of Antibody Concentration per Nanoshell 163
10.6 Discussion of Pitfalls 163
10.7 Statistical Analysis 165
Acknowledgments 166
References 166
CHAPTER 11Environmentally Responsive Multifunctional Liposomes 169
11.1 Introduction 170
11.1.1 Cis-Aconityl Linkage 171
11.1.2 Trityl Linkage 172
11.1.3 Acetal Linkage 172
11.1.4 Polyketal Linkage 172
11.1.5 Vinyl Ether Linkage 172
11.1.6 Hydrazone Linkage 173
11.1.7 Poly(Ortho-Esters) 173
11.1.8 Thiopropionates 173
11.2 Materials 174
11.2.1 Chemicals 174
11.2.2 Syntheses 175
11.2.3 Preparation of the TATp-Bearing, Rhodamine-Labeled11.2.3 Liposomal Formulations 175
11.2.4 Preparation of the TAtp-Bearing, Rhodamine Labeled,11.2.3 pGFP Complexed Liposomal Formulations 175
11.3 Methods 176
11.3.1 Synthesis of Hydrazone-Based mPEG-HZ-PE Conjugates 176
11.3.2 Synthesis of PE-PEG1000-TATp Conjugate 183
11.3.3 In Vitro pH-Dependant Degradation of PEG-HZ-PE11.3.3 Conjugates 184
11.3.4 Avidin-Biotin Affinity Chromatography 184
11.3.5 In Vitro Cell-Culture Study 184
11.3.6 In Vivo Study 185
11.3.7 In Vivo Transfection with pGFP 185
11.4 Discussion and Commentary 185
11.4.1 Synthesis of Hydrazone-Based mPEG-HZ-PE Conjugates 185
11.4.2 Synthesis of PE-PEG1000-TATp Conjugate 186
11.4.3 In Vitro pH-Dependant Degradation of PEG-HZ-PE11.4.3 Conjugates 186
Contents
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11.4.4 Avidin-Biotin Affinity Chromatography 188
11.4.5 In Vitro Cell Culture Study 188
11.4.6 In Vivo Study 188
11.4.7 In Vivo pGFP Transfection Experiment 189
11.5 Conclusion 191
11.7 Summary Points 192
Acknowledgments 192
References 192
CHAPTER 12Biodegradable, Targeted Polymeric Nanoparticle Drug Delivery Formulationfor Cancer Therapy 197
12.1 Introduction 198
12.2 Materials 200
12.2.1 Polymer Synthesis of PLA-PEG and PLGA-PEG 200
12.2.2 Nanoparticle Formation 201
12.2.3 Ligand Conjugation 201
12.2.4 Quantification of Drug Encapsulation 201
12.2.5 Release Experiments 202
12.2.6 Postformulation Treatment 202
12.2.7 Cell Binding and Uptake Experiments 202
12.2.8 Cytotoxicity Experiments 203
12.3 Methods 203
12.3.1 Polymer Synthesis of PLA-PEG and PLGA-PEG 204
12.3.2 Nanoparticle Formation 207
12.3.3 Conjugation of Targeting Ligand 209
12.3.4 Quantification of Drug Encapsulation 211
12.3.5 Drug Release Studies 212
12.3.6 Postformulation Treatment 213
12.3.7 In Vitro Experiments: Cell Binding and Uptake Studies 214
12.3.8 In Vitro Experiments: Cytotoxicity Studies 215
12.4 Data Acquisition, Results, and Interpretation 216
12.4.1 Polymer Characterization 216
12.4.2 Nanoparticle characterization 217
12.4.3 In Vitro Experiments 220
12.5 Discussion and Commentary 222
12.5.1 Particle Size 222
12.5.2 Particle Shape 224
12.5.3 Surface Chemistry 224
12.5.4 Drug Loading 225
12.5.5 Drug Release 226
12.5.6 Active Targeting and Ligand Conjugation 228
12.6 Troubleshooting Tips 230
Contents
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12.7 Application Notes 230
12.8 Summary Points 231
Acknowledgments 231
References 231
CHAPTER 13Porous Silicon Particles for Multistage Delivery 237
13.1 Introduction 238
13.2 Fabrication of PSPs 245
13.2.1 Materials 245
13.2.2 Methods 247
13.2.3 Characterization 251
13.3 Oxidation and Surface Modification with APTES of PSPs 252
13.3.1 Reagents 252
13.3.2 Methods 252
13.4 Fluorescent Dye Conjugation of PSPs 254
13.4.1 Reagents 254
13.4.2 Methodology 254
13.5 Zeta Potential Measurement 254
13.5.1 Equipment 254
13.5.2 Reagents 254
13.5.3 Methodology 254
13.5.4 Results 255
13.6 Count and Size Analysis of PSPs 255
13.6.1 Materials 255
13.6.2 Methods 255
13.6.3 Data Acquisition, Anticipated Results, and Interpretation 256
13.7 Using Inductively Coupled Plasma–Atomic Emission Spectroscopy13.7 (ICP-AES) to Determine the Amount of Degraded Silicon in Solution 257
13.7.1 Materials 257
13.7.2 Methods 258
13.7.3 Data Acquisition, Anticipated Results, and Interpretation 258
13.8 Flow Cytometry to Characterize PSP Shape, Size, and13.8 Fluorescence Intensity 260
13.8.1 Materials 262
13.8.2 Methods 262
13.8.3 Data Acquisition, Anticipated Results, and Interpretation 263
13.9 Loading and Release of Second-Stage NPs from PSPs 264
13.9.1 Loading of NP into PSPs 264
13.9.2 Release of NPs from PSPs 265
13.9.3 Data Acquisition, Anticipated Results, and Interpretation 265
13.10 Discussion and Commentary 267
Acknowledgments 271
Contents
xii
References 271
CHAPTER 14Mathematical Modeling of Nanoparticle Targeting 275
14.1 Introduction 276
14.2 Molecular/Cellular Scale 277
14.2.1 Methods 277
14.2.2 Data Acquisition, Anticipated Results, and Interpretation 280
14.2.3 Discussion and Commentary 280
14.3 Tissue Scale 282
14.3.1 Methods 282
14.3.2 Data Acquisition, Anticipated Results, and Interpretation 284
14.3.3 Discussion and Commentary 284
14.4 Organism Scale 285
14.4.1 Methods 285
14.4.2 Data Acquisition, Anticipated Results, and Interpretation 286
14.4.3 Discussion and Commentary 287
14.5 Model Validation and Application 287
14.5.1 Statistical Guidelines 287
14.6 Summary Points 289
Acknowledgments 290
References 290
CHAPTER 15Techniques for the Characterization of Nanoparticle-Bioconjugates 293
15.1 Introduction 294
15.2 Methods 296
15.2.1 Separation-Based Techniques 296
15.2.2 Scattering Techniques 300
15.2.3 Microscopy 308
15.2.4 Spectroscopic 312
15.2.5 Mass Spectroscopy 317
15.2.6 Thermal Techniques 318
15.3 Summary Points 319
Acknowledgments 320
References 321
About the Editors 333
List of Contributors 334
Index 337
Contents
xiii
C H A P T E R
1Preparation and Characterization of CarbonNanotube-Protein Conjugates
Jonathan S. Dordick,* Dhiral A. Shah, Ravindra C. Pangule, Shyam Sundhar Bale,Prashanth Asuri, Amit Joshi, Akhilesh Banerjee, David Vance, and Ravi S. Kane*
Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY
*Corresponding Authors: Prof. Ravi S. Kane, Department of Chemical and Biological Engineering,Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, Phone: 518-276-2536, Fax:518-276-4030, e-mail: [email protected]; Prof. Jonathan S. Dordick, Department of Chemical and BiologicalEngineering, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, Phone: 518-276-2899, Fax:518-276-2207, e-mail: [email protected]
1
Abstract
This chapter describes methods of immobilizing proteins on carbonnanotubes, using two different routes—physical adsorption and covalentattachment. We also provide an overview on how such conjugates can be char-acterized with the help of various techniques, such as Raman, Fourier trans-form infrared (FT-IR), circular dichroism (CD), and fluorescence spectroscopies,in addition to the standard enzyme kinetic analyses of activity and stability.Both the attachment routes—covalent and noncovalent—could be used to pre-pare protein conjugates that retained a significant fraction of their native struc-ture and function; furthermore, the protein conjugates were operationallystable, reusable, and functional even under harsh denaturing conditions. Thesestudies therefore corroborate the use of these immobilization methods to engi-neer functional carbon nanotube-protein hybrids that are highly active andstable.
Key terms enzyme immobilizationcarbon nanotubesphysical adsorptioncovalent attachmentnanotube solubilization
1.1 Introduction
Nanomaterials, such as carbon nanotubes (CNTs) offer a unique combination of electri-cal, mechanical, thermal, and optical properties [1] that make them promising materialsfor various applications ranging from sensing [2] and diagnostics to biotransformationsand the cellular delivery of peptides and proteins [3, 4]. For instance, Barone et al. [5]have developed carbon nanotube-glucose oxidase conjugates that can act as glucose sen-sors. Recently, Dai and coworkers [2] demonstrated the recognition of monoclonal anti-bodies by a recombinant human antigen immobilized onto carbon nanotubes. Carbonnanotubes have also been used for both biomolecule delivery and targeted therapy.Pantarotto et al. [3] demonstrated that carbon nanotubes functionalized with peptidescan penetrate cell membranes of human and murine fibroblasts, and serve as carriers forbiomolecule delivery. Dai and coworkers [4] observed internalization of nanotube-pro-tein conjugates in nonadherent human cancer cells as well as adherent cell lines. Kam etal. [6] demonstrated that functionalized CNTs could be used to selectively target cancercells and destroy them by irradiating CNTs with near-infrared (NIR) light. These studiesrepresent a fraction of the exciting opportunities at the interface of nanotechnologyand biotechnology. It is, however, important to interface carbon nanotubes withbiomolecules, such as proteins, to realize some of these applications. As a result, variousmethods of functionalization have been developed recently to functionalize CNTs withproteins. In this chapter, we describe three methods of preparing carbon nanotube-pro-tein conjugates, each of them possessing distinct structural, mechanical, and functionalcharacteristics.
Noncovalent attachment is probably the simplest technique for attaching proteinsonto carbon nanotubes. The adsorption of proteins onto CNTs is hypothesized to be aresult of the attractive hydrophobic interactions between carbon nanotubes and pro-teins [7]. This method has been found to preserve a significant fraction of the nativestructural and functional properties of several proteins as well as the physicochemicalproperties of nanotubes [2, 8–10]. The resulting formulations prevail in the form ofaggregates, which can be easily separated from other solution components. However,the limited solubility of these conjugates in water limits their attractiveness for manyapplications in biotechnology [11, 12]. Nevertheless, such conjugates have been used forbiosensing, diagnostics and preparing antifouling nanocomposites films [13].
To overcome the aforementioned limitation of water solubility, Karajanagi et al.have described a simple method that uses proteins to solubilize single-walled carbonnanotubes (SWNTs) in water [14]. Efficient solubilization of SWNTs has previously beenachieved using surfactants [15, 16], polymers [17, 18], single stranded DNA [19], pep-tides [20], and polysaccharides [12, 21]. The direct solubilization of SWNTs using a vari-ety of proteins differing in size and structure is a simple and scalable alternative thatenables the generation of individual nanotube solutions. Moreover, proteins are rich instructure and function and have numerous reactive groups, such as hydroxyls, amines,thiols, carboxylic acids, and others, which can be used as orthogonal reactive handlesfor further functionalization of SWNTs.
Finally, Asuri et al. have developed an alternative method of preparing water-solubleconjugates of carbon nanotubes with a broad range of proteins [22]. CNTs can be acidoxidized to produce hydrophilic carboxylic acid and hydroxyl groups along their side-walls [23, 24], thereby leading to water solubility. Proteins can then be covalentlyattached to oxidized water-soluble CNTs using carbodiimide activation of the carboxylic
Preparation and Characterization of Carbon Nanotube-Protein Conjugates
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acid groups. These water-soluble conjugates not only display low diffusional resistance[25] and high activity with stable protein attachment [26], but also have added advan-tages of high stability and reusability, thereby overcoming the traditional limitations ofwater-soluble proteins. Though the covalent immobilization of proteins onto CNTsleads to stable protein attachment, the chemical modification of the CNTs surface maycompromise the desirable electronic properties of CNTs. Such water-soluble CNT-pro-tein conjugates may find application in fields other than biosensing, for example,biotransformations, biomaterials, medicine, and self-assembled materials.
It is, therefore, clear that many methods have been explored to prepare functionalnanotube-protein conjugates. Each of these methods possesses its own unique set ofadvantages and disadvantages, and the best choice of the method depends on thedesired end application of the hybrid conjugates.
1.2 Materials
Raw and purified HIPCO single-walled carbon nanotubes (SWNTs) (1–1.5 nm diameter,ca. 10 μm length, <35 wt% ash content) were purchased from Unidym (Houston, TX).Multiwalled carbon nanotubes (MWNTs) (10–20 nm diameter, 5–20 µm length, 95wt% purity) were purchased from Nanolab, Inc. (Newton, MA). Enzymes—soybeanperoxidase (SBP), horseradish peroxidase (HRP) and Mucor javanicus lipase (MJL)—werepurchased from Sigma-Aldrich (St. Louis, MO) as salt-free, dry powders. Bicinchoninicacid (BCA) assay kit for determining solution phase protein concentrations waspurchased from Pierce Biotechnology, Inc. (Rockford, IL). Guanidine hydrochloride(GdnHCl), sodium dodecylbenzene sulfonate (NaDDBS), and all other chemicals wereobtained from Sigma. Bovine serum albumin (BSA) was purchased from Fisher ScientificInternational, Inc. (Hampton, NH). All other chemicals were obtained from Sigma-Aldrich (St. Louis, MO). All enzymes and chemicals were used as received without anyfurther purification.
1.3 Methods
1.3.1 Physical Adsorption of Proteins on Carbon Nanotubes
Attachment of proteins to carbon nanotubes via physical adsorption represents a facilemethod of preparing nanotube-protein conjugates, wherein an aqueous dispersion ofSWNTs is mixed with a protein solution to achieve adsorption. The unadsorbed proteinis washed off and nanotube-protein conjugates are then resuspended in aqueoussolution. The detailed procedure is described below:
1. Sonicate a fixed amount of raw SWNTs in dimethylformamide (DMF) at aconcentration of 1 mg/mL for 30 minutes using a bath sonicator (Model 50T, VWRInternational, West Chester, PA) with rated power of 45W to obtain a uniformdispersion in solution.
2. Dispense 1 mL of the resulting SWNT dispersion into an Eppendorf microcentrifugetube, and centrifuge the solution at 8,000 rpm for 1 minute. Remove the supernatantand resuspend the settled SWNTs in an aqueous buffer (50 mM phosphate buffer, pH
1.2 Materials
3
7.0) by vortexing the solution. Repeat this wash procedure at least five more times toremove any residual organic solvent. This gradual change from organic phase to anaqueous phase renders unfunctionalized SWNTs more dispersed in buffer. Finally,disperse 1 mg SWNTs in 500 μL aqueous buffer (15 minutes).
NOTE: The selection of buffer for preparing conjugates is dependent upon the choiceof protein and the retention of its native function in that buffer.
3. Prepare a fresh solution of protein in the aqueous buffer. Add the aqueous dispersionof SWNTs (500 μL, 2 mg/mL) to the protein solution (500 μL), and shake the mixtureon a platform shaker for 2 hours at 200 rpm and room temperature (2 hours 15minutes).
NOTE: In the case of thermally unstable proteins or enzymes undergoing autolysis,such as trypsin, shaking should be carried out at 4°C to prevent deactivation duringincubation.
4. After incubation, centrifuge the SWNT dispersion at about 8,000 rpm for 1 minute tosettle the SWNT-protein conjugates. Carefully decant the supernatant (ca. 800 μL)without loss of any conjugates. Typically, perform six such washes, with fresh bufferadded each time to remove unbound protein (20 minutes).
NOTE: While collecting the supernatant, tilt the microcentrifuge tube and gentlypipette out approximately 800 μL supernatant from close to the tube walls without dis-turbing the settled SWNTs, so that the supernatant does not contain SWNTs, whichcan interfere with BCA assay for protein content determination in supernatants. Aswinging bucket microcentrifuge is ideal for this step, as the SWNTs settle at the bot-tom and not on the walls of the tube after centrifugation. Do not resuspend theSWNT-protein conjugates by vortexing, as this can lead to desorption of the proteinfrom SWNT surface. Resuspend the conjugates by gently inverting and tapping themicrocentrifuge tube containing the conjugates.
5. Analyze the supernatants for protein content using the BCA assay (for proteinconcentration range of 20–2,000 μg/mL) or the micro-BCA assay (for proteinconcentration range of 0.5–20 μg/mL). Determine the amount of protein attachedonto the SWNTs by mass balance. Use the SWNT-protein dispersion for furtheranalysis and characterization. (1 hour 15 minutes) The process flowchart is shown inFigure 1.1.
The total time to carry out the procedure is approximately 5 hours.
1.3.2 Protein Assisted Solubilization of Carbon Nanotubes
For preparation of protein solubilized carbon nanotubes, an aqueous dispersion ofnanotubes is dispensed in a concentrated protein solution and exposed toultrasonication for a predetermined time period. The supernatant, collected aftersequential steps of ultracentrifugation of the CNT-protein dispersion, containsolubilized carbon nanotubes that are stable at room temperature and show no signs ofaggregation. The detailed procedure is described below:
Preparation and Characterization of Carbon Nanotube-Protein Conjugates
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1. Disperse purified SWNTs in DMF at a concentration of 1 mg/mL by sonication,and replace the organic phase gradually with an aqueous phase through repeatedwashing with milliQ water (as stated in section 1.3.1) (45 minutes).
2. Disperse 200 μg of SWNTs in 4-mL protein solution (10 mg/mL) and sonicatethe dispersion of SWNTs for 2 hours using a bath sonicator (Model 50T, VWRInternational, West Chester, PA) with rated power of 45W (2 hours).
3. Ultracentrifuge the dispersed solution at 123,000g for 30 minutes.
4. Carefully collect 60% of the supernatant and ultracentrifuge at 185,000g for 30minutes.
5. Collect 75% of the supernatant that contains protein adsorbed SWNTs. Use thissolution for further analysis and characterization.
The total time to carry out the procedure is approximately 4 hours.
NOTE: The sonication efficiency and, hence, the quality of the dispersion varies withthe volume of the solution sonicated. For best dispersions, use 4 mL volume forsonication.
1.3.3 Covalent Attachment of Proteins onto Carbon Nanotubes
For covalently attaching proteins onto carbon nanotubes, the carbon nanotubes are firstfunctionalized with carboxylic acid groups by acid treatment. The carboxylic acidgroups are then “activated” to form succinimide esters using carbodiimide chemistry[23]. These activated carboxylic groups react with amine groups on proteins enablingthe covalent attachment of proteins onto carbon nanotubes. A detailed description ofthe procedure is given below:
1.3 Methods
5
Calculate the proteinloading on SWNTs by
mass balance
Shake the mixture on aplatform shaker for 2
hours at 200 rpm
Sonicate a 1 mg/mLdispersion of SWNTs
in DMF for 30 min
Mix the SWNTssolution with a freshly
prepared proteinsolution
Centrifuge the SWNT -protein mixture at 8000
rpm for 2 min
Remove thesupernatant and
resuspend the SWNTsin aqueous buffer
Centrifuge 1 ml ofSWNTs dispersion at8000 rpm for 2 min
Disperse the SWNTs in500 µL aqueous buffer
Collect the supernatantand resuspend the
SWNT -proteinconjugates in buffer
Repeat the steps 5 times to removeresidual organic solvent
Repeat the steps 6 times to removeunadsorbed enzyme from solution
Calculate the proteinloading on SWNTs by
mass balance
Shake the mixture on aplatform shaker for 2
hours at 200 rpm
Sonicate a 1 mg/mLdispersion of SWNTsin DMF for 30 min
Mix the SWNTssolution with a freshly
prepared proteinsolution
Centrifuge the SWNT-protein mixture at 8000
rpm for 2 min
Remove thesupernatant and
resuspend the SWNTsin aqueous buffer
Centrifuge 1 ml ofSWNTs dispersion at8000 rpm for 2 min
Disperse the SWNTs in500 L aqueous bufferμ
Collect the supernatantand resuspend the
SWNT-proteinconjugates in buffer
Repeat the steps 5 times to removeresidual organic solvent
Repeat the steps 6 times to removeunadsorbed enzyme from solution
Figure 1.1 Process flowchart for the physical adsorption of proteins onto SWNTs.
1. Sonicate a fixed amount of multiwalled carbon nanotubes (MWNTs) in a mixtureof concentrated sulfuric acid and nitric acid (3:1, v/v; 400 mL/100 mg carbonnanotubes) using a bath sonicator with a rated power of 45W for 3 hours.Periodically replace the contents of the bath with ice cold water to ensure that theMWNT suspension does not get heated up during sonication (3 hours).
NOTE: Acid oxidation not only leads to the functionalization of MWNTs withcarboxylic acid groups, but also causes cutting of MWNTs. Longer sonication timesresult in finer oxidized MWNTs.
2. Add the nanotube-containing acid solution (400 mL) to an ice-cold solution ofmilliQ water (3,600 mL) gradually with constant swirling. Allow 10 to 15 minutes fordissipation of the heat generated on diluting the acid mixture.
3. Filter the solution through a 0.22-μm polycarbonate filter membrane (Isoporemembrane, Millipore) in batches of approximately 200 mL to remove the acid. Aftereach filtration, disperse the nanotube film or bucky paper (a mass of carbonnanotubes tangled with each other to form a film or mat) thus formed in 50-mLmilliQ water by ultrasonication in the bath sonicator for approximately 10 minutes,until the nanotubes are dispersed entirely in solution. Dilute this suspension with150-mL milliQ water (40 minutes).
4. Repeat the ultrasonication/filtration step at least three times until water-solubleMWNTs are obtained and the pH of the filtrate becomes neutral (2 hours).
NOTE: These oxidized and “cut” nanotubes can be stored in aqueous solution(1 mg/mL) at room temperature.
5. After the final filtration, disperse the oxidized nanotubes (2 mg/mL) in MES (2-(N-Morpholino) ethanesulfonic acid) buffer (50 mM, pH 6.2), and add an equalvolume of 400-mM N-hydroxysuccinimide (NHS) in MES buffer (5 minutes).
6. Sonicate the mixture for 30 minutes in a bath sonicator.
7. Add N-ethyl-N’-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDC) (20mM in MES buffer) to the nanotube solution to initiate the coupling of NHS to thecarboxylic groups on the oxidized nanotubes, and stir the mixture at 400 rpm for 30minutes at room temperature.
8. Filter the activated nanotube solution through a polycarbonate filter membrane(0.22 μm) and rinse thoroughly with MES buffer to remove excess EDC and NHS (20minutes).
9. Transfer the nanotube film immediately into a freshly prepared protein solution (2mg/mL, 10 mM phosphate buffer, pH 8.0), and sonicate for few seconds to dispersethe nanotubes in solution.
NOTE: Do not allow the nanotube film to dry out completely on the filter membraneas it may lead to hydrolysis of the active ester and hence decreased attachment of theprotein.
10. Shake the mixture on an orbital shaker at 200 rpm for 3 hours and at roomtemperature to allow the attachment of proteins to the nanotubes.
Preparation and Characterization of Carbon Nanotube-Protein Conjugates
6
NOTE: Proteins such as proteases or thermally unstable proteins require that this stepbe carried out at 4°C to prevent protein deactivation.
11. Filter the nanotube-protein suspension and wash it three times with milliQ water(5-mL/mg nanotubes) and once with 1% Tween-20 (5-mL/mg nanotube) to removeany nonspecifically bound protein (2 hours).
12. Allow flocculates of nanotube-protein conjugates, if any, to settle overnight and usethe supernatant for further experiments.
13. Quantify the amount of immobilized protein by elemental analysis of the oxidizednanotubes and the nanotube-protein conjugates. The schematic of the process ofprotein functionalization on nanotubes is shown in Figure 1.2.
The total time to carry out the procedure is approximately 11 hours.
1.4 Data Acquisition, Anticipated Results, andInterpretation of Data
We have employed various techniques, such as Raman, FT-IR, CD, and fluorescencespectroscopies in addition to the standard enzyme kinetic analyses of activity and stabil-ity, to understand how the attachment onto CNTs influences protein structure andfunction. The choice of technique depends on the method used for protein attach-ment and the resulting characteristics of the formulation (e.g., protein loading anddispersibility). In this section, we discuss these characterization techniques and includeour own data of experiments to enable the reader to evaluate the CNT-protein conju-gates prepared by the previously described methods of protein attachment onto carbonnanotubes.
1.4.1 Characterization of Proteins Physically Adsorbed onto CarbonNanotubes
We have used enzymes as probes of protein structure and function. To measure theretention of enzyme activity upon attachment, it is necessary to quantify the amount ofenzyme physically adsorbed onto carbon nanotubes. Measuring enzyme activity anddetecting the change in its secondary structure by FT-IR spectroscopy before and after
1.4 Data Acquisition, Anticipated Results, and Interpretation of Data
7
H SO : HNO2 4 3
3:1, 3h
CNT
(a) (b)
EDC/NHS
pH 6.2
Protein
NH2
CNT-Protein
Figure 1.2 CNT-protein composites. (a) Schematic of protein functionalization of carbon nanotubes.(b) Photograph of water-soluble MWNTs. (Adapted from Asuri et al. [22].)
adsorption is useful for studying the influence of the hydrophobic nanoscale environ-ment of carbon nanotubes on protein structure and function. Also, enzyme activitymeasurement can be used to determine the stability of enzymes adsorbed ontonanotubes under harsh conditions.
1.4.1.1 Measurement of Loading of Proteins on Carbon Nanotubes by the BCA Assay
The Pierce BCA Protein Assay uses a detergent-compatible formulation based onbicinchoninic acid (BCA) for the colorimetric detection and quantification of total pro-tein. It involves the reduction of Cu2+ to Cu1+ ions by proteins to form a water solublecomplex with BCA that strongly absorbs at 562 nm. Using this assay, the loading of pro-teins on carbon nanotubes is calculated as follows:
Amount of protein loaded per mg SWNT = ⋅ − ⋅∑C V C Vi i j jn
(1.1)
where,
Ci = Initial concentration of protein before exposing it to SWNTs;
Vi = Initial volume of protein solution added to SWNT dispersion;
Cj = Concentration of supernatant in jth wash;
Vj = Volume of supernatant in jth wash;
n = Number of washes performed.
Representative data for the loading of SBP on SWNTs is shown in Figure 1.3(a). Theadsorption of SBP followed a pseudosaturation behavior, with a maximum loading of575 μg SBP/mg SWNTs (Figure 1.3(a)). We observed that adsorbed SBP has a strong affin-ity for the SWNTs, with almost complete adsorption observed within the first minute(data not shown). Protein adsorption was irreversible at lower loadings. For example, at aloading of 250-μg protein/mg SWNT, essentially no protein desorption was observed(Figure 1.3(b)). The AFM images of SWNT-SBP conjugates are shown in Figure 1.3(c) and(d). The globular structures seen on the wire like SWNTs represent SBP molecules. Linescans reveal that a region on the SWNTs that does not contain SBP has a height of 3.7nm, while a region containing SBP has a height of 9.6 nm, the difference (5.9 nm) beingthe height of adsorbed SBP molecules.
1.4.1.2 Retention of Protein Activity Upon Physical Adsorption
Adsorption onto CNTs can influence the structure, function, and stability of proteins.Since the catalytic activity of proteins relies on the retention of their native structure,measurement of catalytic activity can be used to evaluate the influence of the nanoscaleenvironment of a CNT on protein properties. Using enzymes as highly sensitive probesof protein function, we studied the strong influence of the CNT surface on proteinfunction and stability in harsh environments.
Preparation and Characterization of Carbon Nanotube-Protein Conjugates
8
Determination of Protein Activity Upon Physical AdsorptionThe structure, function, and spatial orientation of proteins attached onto carbonnanotubes strongly depends on the interactions of the nanotube surface with proteins.Since the catalytic activity and exquisite selectivity of proteins requires the near com-plete retention of native structure, measurement of enzyme activity can be used to eval-uate the influence of the hydrophobic nanoscale environment of nanotubes on enzymestructure and function. To that end, comparison of the activity of native and immobi-lized enzyme can provide insight into the influence of carbon nanotubes on the reten-tion or loss of native-like enzyme properties.
As an example, the activity of native SBP was measured using p-cresol as the substrate[27]. SBP catalyzes the oxidation of p-cresol in the presence of H2O2 to form fluorescentoligo- and polyphenol products. The initial reaction rates were measured by tracking theincrease in fluorescence of the reaction mixture at excitation and emission wavelengthsof 325 nm and 402 nm, respectively, using an HTS 7000 Plus Bio Assay Reader(Perkin-Elmer, Wellesley, MA). For a typical solution-phase assay, 0.15-µg/mL SBP wasused with 20-mM p-cresol and 0.125-mM H2O2 in a volume of 200 μL. To measure the
1.4 Data Acquisition, Anticipated Results, and Interpretation of Data
9
(a) (b)
(d)(c)
1000
800
600
400
200
00 500
Amount of SBP exposed to SWNTs( g SBP/mg SWNTs)μ
1000 1500 2000 250
300
250
200
150
100
50
00 1 2 3 4 5 6 7
Number of washes
50100
150200
250 nm
0 100 200 300 400nm
0 100 200 300 400nm
nmnm
Figure 1.3 Loading of SBP on SWNTs: (a) Protein loading as a function of amount of SBP exposed toSWNTs. (b) Protein loading as a function of washing with fresh buffer. (c) AFM images of SBP adsorbedonto SWNTs. (d) Surface plot of height image for SBP adsorbed onto SWNTs revealing SBP moleculeson the SWNTs. (Reprinted with permission from Karajanagi et al. . Copyright (2004) American Chemi-cal Society [7].)
activity of SBP adsorbed onto SWNTs, a well-mixed dispersion of SWNT-SBP at a concen-tration of 1.0 mg/mL was prepared in aqueous buffer. For a typical experiment, 0.2–2.5μg of SWNTs were used on the basis of the loading of SBP. It was found that SBP retainedsignificant specific activity at all loadings (Figure 1.4) ranging from 18 to 280 μg SBP/ mgSWNTs. The specific activity of SBP was strongly dependent on the loading; up to 28% ofnative solution activity was obtained at 50% of maximal surface coverage, and this valuedropped to ca. 10% at 3% of maximal surface coverage (Figure 1.4). The increase in spe-cific activity of adsorbed SBP with an increase in the surface coverage on SWNTs may bedue to a higher retention of native structure at higher surface loadings.
Protein Stability under Harsh ConditionsPhysical adsorption of proteins to carbon nanotubes enhances the stability of proteinsin strongly denaturing environments where native proteins undergo substantial deacti-vation. To determine protein stability at elevated temperatures (Figure 1.5(a)), thenanotube-protein conjugates were subjected to these temperature conditions for differ-ent periods of time and cooled in an ice bath. Initial enzymatic reaction rates were thendetermined at room temperature. To determine rate constants in approximately 100%methanol (Figure 1.5(b)), the initial rates were measured in methanol as a functionof incubation time. The deactivation constant was determined from the slope of astraight-line fit through the plot of loge (% activity retained) versus time.
1.4.1.3 Determination of Protein Secondary Structure Using Fourier TransformInfrared (FT-IR) Spectroscopy
FT-IR spectroscopy is an established tool for the structural characterization of proteins[29]. The secondary structure of a protein can be quantitatively determined from a spec-trum by considering the amide I region, between 1,600 and 1,700 cm-1. This region,which consists mainly of the C-O stretching vibration of the backbone peptide bonds inproteins, was used to obtain the α helix and β sheet contents of the protein [30, 31]. We
Preparation and Characterization of Carbon Nanotube-Protein Conjugates
10
Fraction of maximal coverage ofenzymes on SWNTs
0.0 0.1 0.2 0.3 0.4 0.5 0.60
5
10
15
20
25
30
35
Perc
ent
nativ
esp
ecifi
cac
tivity
reta
ined
Figure 1.4 Enzymatic activity retained as a function of the surface coverage of SBP adsorbed onSWNTs (▲). (Reprinted with permission from Karajanagi et al. [7]. Copyright (2004) AmericanChemical Society.)
used FT-IR spectroscopy to compare the secondary structure of proteins before and aftertheir adsorption onto carbon nanotubes. The differences in secondary structure betweenthe soluble and adsorbed states are represented by the simple sum of magnitudes ofchanges in α helix and β sheet contents. For example, SBP showed a total change in α
helical and β sheet content of 13% (Table 1.1), which suggests that SBP retains much ofits native structure and activity upon absorption onto SWNTs.
1.4.2 Characterization of Protein-Solubilized Carbon Nanotubes
The aggregation state of the protein solubilized carbon nanotube dispersions can becharacterized by ultraviolet-visible (UV-Vis) and Raman spectroscopy. These methodscan be used effectively to distinguish between solubilized and nonsolubilized carbonnanotubes. We describe the use of these two techniques to characterize the solubilizedCNTs.
1.4.2.1 Characterization of Carbon Nanotube Dispersions Using UV-Vis Spectroscopy
The UV-Vis absorption spectra of dispersions of SWNTs are known to be sensitive totheir aggregation state [15]. The UV-Vis spectrum for SWNTs in water in the absence of adispersing agent was essentially featureless, which indicates the presence of aggregatesof SWNTs (data not shown). In contrast, the UV-Vis spectra for solutions of SWNTs
1.4 Data Acquisition, Anticipated Results, and Interpretation of Data
11
Table 1.1 Secondary Structure Percentages of SBP in Solution andAbsorbed onto SWNTs, as Determined by FT-IR Spectroscopy Calculatedfrom the Amide I Spectra
Sample % α Helix % β Sheet
Native solution of SBP 36.1 ± 1.2 25.1 ± 2.5SBP absorbed onto SWNTs 27.9 ± 4.1 20.6 ± 6.9
(Adapted from Karajanagi et al. [7])
0 501.0
10.0
100.0
Perc
ent
activ
ityre
tain
ed
100 150 200 250
Min
0 501.0
10.0
100.0
Perc
ent
activ
ityre
tain
ed
100 150 200 250
Min
(a) (b)
Figure 1.5 Time-dependent deactivation of native SBP (�) and SBP on SWNTs (�) (a) at 95°C and (b)in 100% methanol. The activities are normalized relative to the initial activity (activity at t = 0 min).Figure 1.5(b) does not contain % activity data for native SBP as it shows no activity in 100% methanol.(Reprinted with permission from Asuri et al. [28]. Copyright (2006) American Chemical Society.)
obtained using the proteins BSA and MJL exhibited sharp and well-resolved peaks(Figure 1.6). These sharp van Hove peaks are a characteristic of aqueous solutionscontaining debundled, individually dispersed SWNTs. The UV-Vis spectrum for SWNTsdispersed in water using NaDDBS also shows similar sharp features (Figure 1.6). Wenote that the spectra for SWNT-BSA and SWNT-MJL show peaks in the region beyond900 nm that are red-shifted by approximately 10 to 15 nm with respect to those forSWNT-NaDDBS. This shift may be attributed to the greater accessibility of water to theSWNT surface for SWNT-BSA and SWNT-MJL than for SWNT-NaDDBS. It has beenshown [32] that proteins can form a more porous layer on the SWNT surface than surfac-tants, thereby permitting water and other small molecules to associate with the surface.
1.4.2.2 Raman Spectroscopy to Probe Aggregation State of SWNTs
Raman spectroscopy is a versatile tool, which enables us to probe the aggregation state ofSWNTs in solutions. In the case of protein-solubilized SWNT dispersions, the radialbreathing mode (150–350 cm–1) and tangential mode observations can be used asindicators of the quality of nanotube dispersion. To obtain the Raman spectra of thesolubilized SWNT-BSA conjugates, 10 μg of the conjugates were placed on a cleaned sili-con substrate and samples were analyzed using a laser excitation at 785 nm at a power of10 mW, with a 50x lens. (Spectra were recorded from 0–3000 cm–1 for 4 minutes). Thewavenumber calibration was carried out using the 521-cm–1 line of silicon substrate as areference. The relative intensities of Raman peaks in the region between 230 and 270cm–1 were found to be good indicators of the nanotube dispersion because of the changein Raman spectrum depending on their dispersed state. Specifically, in the aggregatedstate, (10,2) nanotubes are in resonance and (10,5) nanotubes are off resonance, whilewhen SWNTs are dispersed, (10,5) nanotubes are in resonance and (10,2) nanotubes areoff resonance. Accordingly, we see a peak at 267 cm–1 for SWNT aggregates, whereassolubilized SWNT-BSA conjugates show no peak at 267 cm-1 but a prominent peak at 234cm–1 (Figure 1.7(a)). Furthermore, the peak corresponding to the tangential mode (cen-tered at 1,591 cm–1) for soluble SWNT-BSA was narrower than that for the aggregated
Preparation and Characterization of Carbon Nanotube-Protein Conjugates
12
400 600
Wavelength (nm)
Nor
mal
ized
abso
rban
ce
800 10000.0
0.2
0.4
0.6
0.8
1.0
Figure 1.6 UV-Vis absorption spectra of SWNTs dispersed in water using NaDDBS (dashed line), BSA(solid line), and MJL (dash-dot line) normalized at 410 nm. (Reprinted with permission fromKarajanagi et al. [14]. Copyright 2006 American Chemical Society.)
SWNTs, with a decrease in the full width at a half-maximum of approximately 5 cm–1
(Figure 1.7(b)), which is in agreement with similar observations for solutions containingindividually dispersed SWNTs [20, 33, 34].
1.4.3 Characterization of Covalently Attached Carbon Nanotube-ProteinConjugates
We determined the retention of protein structure and function upon covalent attach-ment to carbon nanotubes using Hammett analysis of protein activity as well as spectro-scopic techniques, such as CD and fluorescence spectroscopies. Structural analysis byCD or fluorescence spectroscopy is not possible for conjugates prepared by physicaladsorption of proteins onto bundles of nanotubes or for covalent MWNT-protein conju-gates because of interference from the carbon nanotubes. On the other hand, because ofthe higher solubility and higher protein loading obtained in case of covalent attachmentof proteins to oxidized SWNTs, CD, and fluorescence measurement-based structuralstudies are possible. The activity measurements of the nanotube-protein conjugatesindicated that the conjugates demonstrated not only enhanced stability in harshconditions, but also operational and storage stability.
1.4.3.1 Hammett Analysis for Protein Structure-Activity Relationship
It is often important to study the structural perturbations of the protein to further probethe effects of immobilization. However, analyses of proteins on MWNTs, such as CD andFT-IR spectroscopy, are hindered by the strong absorbance and intrinsic fluorescence ofnanotubes. Hammett analysis, on the other hand, is a well-established kinetic techniqueto probe an enzyme’s transition state structure [27]. In the case of SBP catalysis, theHammett coefficient ρ provides a measure of the sensitivity of SBP’s catalytic efficiencyto the electronic nature of substituents on phenolic substrates (electron-donating orelectron-withdrawing), as reflected in the values of their substituent electronic parame-ter σ. Positive values of σ represent electron withdrawal by the substituent from the aro-matic ring, whereas negative values indicate electron release to the ring. Deviation in ρ
values for SBP bound to a support from that for the native enzyme in aqueous buffer
1.4 Data Acquisition, Anticipated Results, and Interpretation of Data
13
0.0160 180 200 220 240 260 280 300
0.2
0.4
0.6
0.8
1.0
1.2
Wavenumber (cm )−1
−1 −1
(a) (b)
234 cm 267 cm
0.0
1560 1580
Nor
mal
ized
inte
nsity
Nor
mal
ized
inte
nsity
1600 1620
0.2
0.4
0.6
0.8
1.0
1.2
Wavenumber (cm )−1
−11591 cm
Figure 1.7 Raman spectroscopic analysis of SWNT-BSA conjugates (solid line) and SWNTs (dashedline) in (a) Radial breathing mode, (b) Tangential mode at 785-nm excitation. (Reprinted with permis-sion from Karajanagi et al. [14]. Copyright 2006 American Chemical Society.)
would indicate that the active site structure of the enzyme is perturbed by adsorptiononto the support.
logVKM
max constant⎛⎝⎜
⎞⎠⎟ = ⋅ +σ ρ (1.2)
To that end, we determined the Hammett coefficient, ρ, based on a modified form ofthe Hammett equation for SBP (1.2), using a series of phenolic substrates, p-OC2H5,p-CH3, p-CH2OH, and p-Cl with different values of the electronic parameter (σ) varyingfrom -0.24 to +0.23 [27].1 The standard kinetic parameters—maximum reaction rate(Vmax) and Michaelis constant (KM)—were determined for the different substrates usingnonlinear Michaelis-Menten fits. Figure 1.8 depicts the Hammett analysis for native SBPand MWNT-SBP in aqueous buffer. Interestingly, the Hammett coefficients for native
and immobilized SBP are essentially identical. The comparable values of ρ indicate thatthe differences in the active site structure for native and immobilized SBP are minimal;therefore, the mechanism of catalysis for MWNT-SBP is similar to that for native SBP.Thus, the high retention of catalytic activity for the MWNT-SBP conjugates is consistentwith the enzyme retaining its intrinsic active site structure throughout the attachmentprocess.
1.4.3.2 Determination of Protein Secondary Structure Using Circular Dichroism (CD)Spectroscopy
CD spectroscopy is used for studying the conformational stability of a proteinunder harsh conditions—thermal stability, pH stability, and stability against chemicaldenaturants. CD measures the difference in absorbance of a sample between left-hand polarized light and right-hand polarized light; these differences arise because of
Preparation and Characterization of Carbon Nanotube-Protein Conjugates
14
−0.3 −0.2−6.2
−6.0
−5.8
−5.6
−5.4
−5.2
−5.0
−4.8
−4.6
−4.4
log
(V/K
)m
axM
−0.1 0.0 0.1 0.2 0.3σ
Figure 1.8 Influence of the substituent electronic parameter, σ, on the catalytic efficiency of nativeSBP (�) and MWNT-SBP conjugates (�) in aqueous buffer. Slope of the lines gives the Hammett coeffi-cient in each case: ρ for native SBP = –1.6 ± 0.1; ρ for MWNT-SBP = –1.5 ± 0.2. (Adapted from Asuri etal. [22].)
1 The values of the electronic parameter (σ) for p-OC2H5, p-CH3,p-CH2OH, and p-Cl are –0.24, –0.17,0.00, and 0.23 respectively.
structural asymmetry in a molecule. Secondary protein structure is usually comprised ofα helices and β sheets, each producing a characteristic spectrum in the far-UV range(190–250 nm). α helices produce a spectrum with valleys around 208 and 222 nm, whileβ sheets show a single valley around 215 nm. As proteins lose their native structure andbecome less ordered, the absence of regular structure is reflected in zero CD intensity.Thus, by measuring the far-UV CD spectrum of a protein before and after attachmentonto nanotubes, one can get an idea of how the structure of the protein has been altered.Using data processing software that can analyze a CD spectrum and determine the rela-tive content of α helix and β sheet, we determined that HRP attached to SWNTs retained68% of its native α helix content (Figure 1.9).
We used CD spectroscopy to monitor the change in the secondary structure of HRPupon exposure to varying concentrations of GdnHCl denaturant and high tempera-tures. The secondary structure of HRP and SWNT-HRP conjugates were thus monitoredby CD, using a protein concentration of 0.05 mg/mL, in the presence or absence ofdenaturant. After equilibrating the samples with GdnHCl for 24 hours, CD spectra weremeasured (Figure 1.10(b)). The concentration of GdnHCl required to denature the pro-tein by 50% in the sample (Cm) increased from 1.6 to 2.4M as a result of conjugation. Forthermal denaturation, the temperature was slowly raised (0.5°C/min) from 20°C to 99°Cwhile spectra were taken (Figure 1.10(a)). The temperature required to unfold the pro-tein by 50% in the sample (Tm) increased from 79°C to 92°C for the SWNT-HRP conju-gate. Characterization by CD spectroscopy therefore revealed a substantial increase inprotein stability under stronger denaturing conditions and higher temperatures whencovalently attached to SWNTs.
1.4.3.3 Characterization of Protein Tertiary Structure Using Tryptophan Fluorescence
Proteins contain three aromatic amino acid residues (tryptophan, tyrosine, andphenylalanine), which contribute to their intrinsic fluorescence. In particular, the polar-ity and charge densities surrounding tryptophan residues influence both the fluores-cence intensity and maximal emission fluorescence wavelength (λmax). As the proteindenatures, losing its tertiary structure, the environment around buried tryptophan resi-
1.4 Data Acquisition, Anticipated Results, and Interpretation of Data
15
200 210 220 230 240 250
−60
−40
−20
0
Ellip
ticity
(deg
rees
10)
×3
20
260
Wavelength (nm)
Figure 1.9 Far-UV CD spectra of native HRP (�), SWNT-HRP (�), and bare SWNTs (�). (Reprintedwith permission from Asuri et al. [35]. Copyright 2007 American Chemical Society.)
dues changes drastically, eventually leading to their exposure to solution. Thus, uponprotein denaturation, the fluorescence intensities and tryptophan emission wavelengthtend toward those of free tryptophan in solution; structural changes can thus be inferredfrom alteration of the tryptophan’s microenvironment.
As an example, the protein HRP contains one buried tryptophan residue at position117 [36]. When GdnHCl was used as the denaturant (Figure 1.11), the fluorescenceintensities and λmax values for both native HRP and SWNT-HRP conjugate were lowerthan those for free L-tryptophanamide when excited at 283 nm at lower Gdn HCIconcentrations [27, 36]; however, at higher GdnHCl concentrations, both the valuesapproached those of L-tryptophanamide, indicating that HRP’s tryptophan residue wasnow more accessible to the solvent due to protein denaturation. The SWNT-HRP conju-gates showed a more gradual increase toward the values of L-tryptophanamide thannative HRP, indicating that they are more stable under denaturing conditions thannative HRP.
Preparation and Characterization of Carbon Nanotube-Protein Conjugates
16
0.0
0.2
0.4
0.6
0.8
1.0
0 1[GdnHCI] (M)
Frac
tion
dena
ture
d
2 3 4 50.0
0.2
0.4
0.6
0.8
1.0
20 40Temperature (°C)
Frac
tion
dena
ture
d
60 80 100
(a) (b)
Figure 1.10 Fraction of HRP denatured determined by monitoring the CD signal at 222 nm of nativeHRP (�) and SWNT-HRP (�) as a function of (a) GdnHCl concentration and (b) solution temperature.(Reprinted with permission from Asuri et al. [35]. Copyright 2007 American Chemical Society.)
20
30
40
50
60
0 1[GdnHCI] (M)
Flur
esce
nce
inte
nsity
2 3 4 5330
335
340
345
350
355
360
0 1[GdnHCI] (M)
λ(n
m)
max
2 3 4 5
(a) (b)
Figure 1.11 (a) Fluorescence intensity (excitation at 283 nm and emission at λmax) and (b) λmax ofL-tryptophanamide (�), native HRP (�), and SWNT-HRP (�) as a function of GdnHCl concentration.(Reprinted with permission from Asuri et al. [35]. Copyright 2007 American Chemical Society.)
1.4.3.4 Thermostabilization of Proteins Via Covalent Attachment onto CarbonNanotubes
Exposure of proteins to high temperatures can lead to irreversible unfolding and deactiva-tion, posing a critical limitation to their commercial use. We have found that covalentattachment of proteins onto MWNTs leads to thermostabilization of the protein. There isa certain optimal temperature (Topt) at which the protein’s catalytic activity is at itsmaximum, beyond which the protein unfolds and gets deactivated irreversibly. Thethermostabilization of proteins upon immobilization causes an elevation in Topt values.While the Topt for native SBP was found to be approximately 75°C, the MWNT-SBP conju-gates displayed a Topt of approximately 90°C (Figure 1.12), which is close to the nativemelting temperature of SBP (Tm = 90.5°C) [37]. This enhanced stability of MWNT-SBPleads to a 2.5-fold increase in the maximal initial reaction rate at 90°C as compared to thatof native SBP at 75°C, thus rendering the protein formulation well suited for applicationswhere harsh conditions are required.
1.4.3.5 Operational and Storage Stability of Carbon Nanotube-Enzyme Conjugates
Two other issues concerning the commercial use of native enzymes in biocatalysis are dif-ficulty of enzyme reuse and loss of enzymatic activity on prolonged storage. While mac-roscopic supports provide ease of separation and reusability of immobilized enzymes,stabilization provided by such supports is significantly less compared to nanoscale sup-ports [28]. On the other hand, use of inherently long oxidized MWNTs for attachingenzymes not only stabilizes enzymes under different reaction and storage conditions butalso allows easy recovery of conjugates from reaction mixture through filtration. Amat-like film forms after filtering the reaction mixture through the filter membrane; thisfilm can be redispersed in an aqueous buffer by minimal sonication. For example, SBP,which was covalently attached to MWNT, retained about 70% of its initial activity evenafter being reused over 100 times (Figure 1.13(a)). Additionally, such conjugates werefound to be stable for an extended period. Even after 30 days, the MWNT-SBP conjugatesretained ca. 70% of their initial activity (Figure 1.13(b)). On the other hand, native SBPretained only about 30% of its initial activity. These observations indeed suggest that
1.4 Data Acquisition, Anticipated Results, and Interpretation of Data
17
0
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200
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400
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600
20 40 60Temperature (°C)
Initi
alra
te(m
Mm
gs
)−1
−1
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Figure 1.12 Influence of temperature on the kinetics of native SBP (�) and MWNT-SBP (�) in aque-ous buffer. (Adapted from Asuri et al. [22].)
nanoscale supports, such as MWNTs, make the enzyme formulation reusable andstorage compatible.
1.5 Discussion and Commentary
As discussed in the previous sections, characterization of CNT-protein conjugates exhib-its the subtle differences observed due to these different methods of protein immobiliza-tion on CNTs. Biofunctionalization of CNTs and characterization of resultant hybridmaterial has been carried out for various reasons. First, it is of great interest to study howdifferent biomolecules interact with carbon nanotubes compared to conventional microor macroscale supports. For this study, biomolecules were interfaced with nanotubesthrough physical adsorption or covalent attachment. Second, use of CNTs, as drug deliv-ery vehicles or for construction of self-assembled nanoscaled superstructures, requiresthem to be water soluble. The amphiphilic nature of biomolecules can be exploited insolubilizing CNTs. Additionally, these biofunctionalized CNTs can be used in a widerange of applications, which include biosensing, bioelectrochemistry, biomedicine,and intracellular delivery of peptides and proteins. In the course of preparing suchnanobiocomposite materials and realizing their potential applications, we have criti-cally optimized our protocols to overcome some of the problems that can occur withthese techniques. In this section, we discuss some precautions to take while preparingnanotube-protein conjugates.
CNTs, being in the form of clumpy or fluffy black powder, should be handledusing personal protective equipment and in safety hoods with adequate ventilation. Ifinhaled, remove to fresh air. If breathing difficulties persist, get medical attention. Incase of contact, immediately flush eyes or skin with plenty of water for at least 15 min-utes. If irritation develops or persists, get medical attention. During physical adsorptionof proteins, we have observed that protein adsorption occurs in the initial 5 to 10 min-utes of mixing CNTs and protein solutions. Therefore, before mixing these solutions, itis necessary to achieve a uniform dispersion of CNTs through effective sonication. As anadditional precaution, it is advisable to thaw the protein-containing vial after removing
Preparation and Characterization of Carbon Nanotube-Protein Conjugates
18
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Average of every 5 cycles
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Days
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activ
ityre
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13 20 25 30
(a) (b)
Figure 1.13 Operational and storage stability of MWNT-SBP. (a) Reusability of MWNT-SBP conju-gates. (b) Retention of enzymatic activity in aqueous buffer at room temperature—native SBP (�) andMWNT-SBP (�). (Adapted from Asuri et al. [22].)
it from storage temperature of 4°C or –20°C. This is to ensure that the protein powderdoes not pick up unwanted moisture on exposure to air.
As a common safety practice, it is recommended to handle acids in fume hoods whilecarrying out acid oxidation of CNTs. During the sonication step, intermittent swirling ofnanotube-acid mixture would maintain well-mixed reaction conditions. The rise intemperature due to exothermic acid oxidation and sonication leads to heating up ofwater bath, which could cause excessive oxidation of CNTs and hence formation of fine,non-recoverable particles. Therefore, periodic replacement of water in the bath withice-cold water is necessary for maintaining desired operating conditions. Filtration ofCNTs after acid oxidation leads to formation of a densely packed nanotube mat. A sim-plistic approach to get uniform nanotube suspension would be to disperse this nanotubefilm in enough volumes of milliQ water by sonication. After ester functionalization andfiltration of oxidized CNTs, ensure that the filtered CNTs film does not dry outcompletely; disperse the film immediately in protein solution. The pH of the bufferused for carrying out EDC-NHS chemistry was found to govern the extent of esterfunctionalization onto carbon nanotubes. While a pH range of 4 to 7 is suitable, lowerpH conditions results in higher functionalization and hence higher protein attachment.
There are a few notable differences between the three methods of nanotube-proteinpreparation, and the choice of one over the other is governed by the properties of conju-gates desired and their end application. Some of the differences between physicaladsorption of proteins onto CNTs, protein solubilization of CNTs, and covalent attach-ment methods of proteins onto CNTs are listed in Table 1.2.
Troubleshooting Table
Problem Explanation Potential Solution
Low catalytic activity of proteinsupon covalent attachment.
Low protein attachment onto oxidized CNTsin EDC-NHS reaction steps.
Prolonged exposure of active ester to air canlead to its hydrolysis. Add protein solutionimmediately after nanotube activation.
Presence of CNT aggregates afteracid oxidation and filtration steps.
Inefficient oxidation of CNTs. Increase acid treatment duration.
1.6 Applications Notes
The methods of noncovalent and covalent functionalization of carbon nanotubes withproteins have been used in numerous applications two of which are highlighted in this
1.6 Applications Notes
19
Table 1.2 General Comparison Between the Three Methods of Protein Attachment onto CNTs
Physical Adsorption of Proteins onto CNTs Protein Solubilization of CNTsCovalent Attachment of Proteins ontoCNTs
Ease of attachment Ease of attachment Cumbersome with many steps involvedFacile method of attachment preservesnative structural and functional properties ofboth CNTs and proteins
Ultrasonication can lead to proteindenaturation
Chemical modification of CNTs can com-promise its native electronic andmechanical properties
Leaching of proteins upon agitation andstorage
Leaching of proteins upon agitationand storage
No leaching effect observed
Conjugates present in aggregate form Conjugates are water-soluble Conjugates are water-solubleConjugates can be separated fromsolution by centrifugation
Conjugates can be separated fromsolution by filtration
Conjugates can be separated from solu-tion by filtration
section. As our first example, we consider the role of nanobiocomposites in carrying outbiotransformation in biphasic medium wherein phase transfer biocatalysis involves themass transfer of water-insoluble substrates from organic to aqueous phase. Therefore,interfacial adsorption of enzymes is desired to carry out biotransformations at the aque-ous-organic interface. We have demonstrated that SWNTs along with the attached pro-tein can be directed to aqueous-organic interfaces with the aid of surfactants [38].SWNTs as a protein support not only provide high intrinsic surface area but also over-come any intraparticle diffusional limitations that restrict use of enzymes in biphasicsystem. We showed that physical adsorption increased specific enzyme activity by threeorders of magnitude as compared to native enzymes in aqueous phase, with enhancedstability at high temperatures. Thus, the nanotube-mediated interfacial assembly ofenzymes can be very advantageous in directing greater amounts of enzymes from thebulk aqueous phase to the interface and in increasing the stability of enzymes againstinactivation.
The procedure of covalent attachment of proteins onto carbon nanotubes has beensuccessfully employed to produce highly active and stable DNAzyme-carbon nanotubehybrids. Certain small single-stranded DNA fragments possess catalytic activity (e.g.,endonuclease-type activity) and are known as DNAzymes [39]. Yim et al. covalentlyattached streptavidin to acid-treated MWNTs using EDC-NHS chemistry, followedby the binding of biotinylated DNAzyme to yield MWNT-DNAzyme conjugates thatwere soluble in aqueous buffer [40]. The MWNT-DNAzyme conjugates followedMichaelis-Menten kinetics under the conditions where substrate concentration ishigher than that of DNAzyme (Figure 1.14). Additionally, this hybridization led to aformulation providing very high turnover numbers, without the need for substrate-DNAzyme hybridization between each catalytic event. Conjugating such DNAzymeswith nanomaterials can be of potential use in the development of biosensors to detectmetal ions and nucleic acids as well as in designing strategies for directing nanoparticleassembly [41, 42].
Preparation and Characterization of Carbon Nanotube-Protein Conjugates
20
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6 8 10 12 14 16[Substrate] ( M)μ
Initi
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in/m
g)
Figure 1.14 Catalytic activity of MWNT-DNAzyme conjugates. The line represents a nonlinear fit ofthe Michaelis-Menten expression to the data. Inset shows analysis of extent of conversion offluorescently labeled substrate DNA by polyacrylamide gel electrophoresis (PAGE), with upper bandrepresenting uncleaved DNA and lower band representing cleaved fragments. (Reprinted with permis-sion from Yim et al. [40]. Copyright 2005 American Chemical Society.)
1.7 Summary Points
Physical adsorption of proteins onto CNTs is a simple and effective method for prepar-ing nanotube-protein conjugates without any modification of electronic and mechani-cal properties of CNTs.
Protein assisted solubilization of CNTs can be important for biomedical applications,such as biomedical devices, cellular delivery; besides, the wide variety of functionalgroups on adsorbed proteins can act as orthogonal reactive handles for thefunctionalization of CNTs.
Water-soluble CNT-protein conjugates, prepared by acid oxidation of CNTs andcovalent attachment of proteins, possess high enzyme activity, high stability andreusability, and low diffusional resistance; these conjugates can find application inbiomaterials, biotransformations, medicine and self-assembled materials.
Acknowledgments
The methods presented here would not have been possible without the dedicated workof Dr. Sandeep S. Karajanagi, Dr. Tae-Jin Yim, and Dr. Dae-Yun Kim who took part in theoriginal investigations. We also thank Dr. Cerasela Zoica Dinu and Dr. Guangyu Zhu forinsightful discussions and comments.
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